[petsc-users] SuperLU_dist issue in 3.7.4 failure of repeated calls to MatLoad() or MatMPIAIJSetPreallocation() with the same matrix
Barry Smith
bsmith at mcs.anl.gov
Mon Oct 24 06:27:06 CDT 2016
Anton,
Sorry for any confusion. This doesn't resolve the SuperLU_DIST issue which I think Hong is working on, this only resolves multiple loads of matrices into the same Mat.
Barry
> On Oct 24, 2016, at 5:07 AM, Anton Popov <popov at uni-mainz.de> wrote:
>
> Thank you Barry, Satish, Fande!
>
> Is there a chance to get this fix in the maintenance release 3.7.5 together with the latest SuperLU_DIST? Or next release is a more realistic option?
>
> Anton
>
> On 10/24/2016 01:58 AM, Satish Balay wrote:
>> The original testcode from Anton also works [i.e is valgrind clean] with this change..
>>
>> Satish
>>
>> On Sun, 23 Oct 2016, Barry Smith wrote:
>>
>>> Thanks Satish,
>>>
>>> I have fixed this in barry/fix-matmpixxxsetpreallocation-reentrant (in next for testing)
>>>
>>> Fande,
>>>
>>> This will also make MatMPIAIJSetPreallocation() work properly with multiple calls (you will not need a MatReset()).
>>>
>>> Barry
>>>
>>>
>>>> On Oct 21, 2016, at 6:48 PM, Satish Balay <balay at mcs.anl.gov> wrote:
>>>>
>>>> On Fri, 21 Oct 2016, Barry Smith wrote:
>>>>
>>>>> valgrind first
>>>> balay at asterix /home/balay/download-pine/x/superlu_dist_test
>>>> $ mpiexec -n 2 $VG ./ex16 -f ~/datafiles/matrices/small
>>>> First MatLoad!
>>>> Mat Object: 2 MPI processes
>>>> type: mpiaij
>>>> row 0: (0, 4.) (1, -1.) (6, -1.)
>>>> row 1: (0, -1.) (1, 4.) (2, -1.) (7, -1.)
>>>> row 2: (1, -1.) (2, 4.) (3, -1.) (8, -1.)
>>>> row 3: (2, -1.) (3, 4.) (4, -1.) (9, -1.)
>>>> row 4: (3, -1.) (4, 4.) (5, -1.) (10, -1.)
>>>> row 5: (4, -1.) (5, 4.) (11, -1.)
>>>> row 6: (0, -1.) (6, 4.) (7, -1.) (12, -1.)
>>>> row 7: (1, -1.) (6, -1.) (7, 4.) (8, -1.) (13, -1.)
>>>> row 8: (2, -1.) (7, -1.) (8, 4.) (9, -1.) (14, -1.)
>>>> row 9: (3, -1.) (8, -1.) (9, 4.) (10, -1.) (15, -1.)
>>>> row 10: (4, -1.) (9, -1.) (10, 4.) (11, -1.) (16, -1.)
>>>> row 11: (5, -1.) (10, -1.) (11, 4.) (17, -1.)
>>>> row 12: (6, -1.) (12, 4.) (13, -1.) (18, -1.)
>>>> row 13: (7, -1.) (12, -1.) (13, 4.) (14, -1.) (19, -1.)
>>>> row 14: (8, -1.) (13, -1.) (14, 4.) (15, -1.) (20, -1.)
>>>> row 15: (9, -1.) (14, -1.) (15, 4.) (16, -1.) (21, -1.)
>>>> row 16: (10, -1.) (15, -1.) (16, 4.) (17, -1.) (22, -1.)
>>>> row 17: (11, -1.) (16, -1.) (17, 4.) (23, -1.)
>>>> row 18: (12, -1.) (18, 4.) (19, -1.) (24, -1.)
>>>> row 19: (13, -1.) (18, -1.) (19, 4.) (20, -1.) (25, -1.)
>>>> row 20: (14, -1.) (19, -1.) (20, 4.) (21, -1.) (26, -1.)
>>>> row 21: (15, -1.) (20, -1.) (21, 4.) (22, -1.) (27, -1.)
>>>> row 22: (16, -1.) (21, -1.) (22, 4.) (23, -1.) (28, -1.)
>>>> row 23: (17, -1.) (22, -1.) (23, 4.) (29, -1.)
>>>> row 24: (18, -1.) (24, 4.) (25, -1.) (30, -1.)
>>>> row 25: (19, -1.) (24, -1.) (25, 4.) (26, -1.) (31, -1.)
>>>> row 26: (20, -1.) (25, -1.) (26, 4.) (27, -1.) (32, -1.)
>>>> row 27: (21, -1.) (26, -1.) (27, 4.) (28, -1.) (33, -1.)
>>>> row 28: (22, -1.) (27, -1.) (28, 4.) (29, -1.) (34, -1.)
>>>> row 29: (23, -1.) (28, -1.) (29, 4.) (35, -1.)
>>>> row 30: (24, -1.) (30, 4.) (31, -1.)
>>>> row 31: (25, -1.) (30, -1.) (31, 4.) (32, -1.)
>>>> row 32: (26, -1.) (31, -1.) (32, 4.) (33, -1.)
>>>> row 33: (27, -1.) (32, -1.) (33, 4.) (34, -1.)
>>>> row 34: (28, -1.) (33, -1.) (34, 4.) (35, -1.)
>>>> row 35: (29, -1.) (34, -1.) (35, 4.)
>>>> Second MatLoad!
>>>> Mat Object: 2 MPI processes
>>>> type: mpiaij
>>>> ==4592== Invalid read of size 4
>>>> ==4592== at 0x5814014: MatView_MPIAIJ_ASCIIorDraworSocket (mpiaij.c:1402)
>>>> ==4592== by 0x5814A75: MatView_MPIAIJ (mpiaij.c:1440)
>>>> ==4592== by 0x53373D7: MatView (matrix.c:989)
>>>> ==4592== by 0x40107E: main (ex16.c:30)
>>>> ==4592== Address 0xa47b460 is 20 bytes after a block of size 28 alloc'd
>>>> ==4592== at 0x4C2FF83: memalign (vg_replace_malloc.c:858)
>>>> ==4592== by 0x4FD121A: PetscMallocAlign (mal.c:28)
>>>> ==4592== by 0x5842C70: MatSetUpMultiply_MPIAIJ (mmaij.c:41)
>>>> ==4592== by 0x5809943: MatAssemblyEnd_MPIAIJ (mpiaij.c:747)
>>>> ==4592== by 0x536B299: MatAssemblyEnd (matrix.c:5298)
>>>> ==4592== by 0x5829C05: MatLoad_MPIAIJ (mpiaij.c:3032)
>>>> ==4592== by 0x5337FEA: MatLoad (matrix.c:1101)
>>>> ==4592== by 0x400D9F: main (ex16.c:22)
>>>> ==4592==
>>>> ==4591== Invalid read of size 4
>>>> ==4591== at 0x5814014: MatView_MPIAIJ_ASCIIorDraworSocket (mpiaij.c:1402)
>>>> ==4591== by 0x5814A75: MatView_MPIAIJ (mpiaij.c:1440)
>>>> ==4591== by 0x53373D7: MatView (matrix.c:989)
>>>> ==4591== by 0x40107E: main (ex16.c:30)
>>>> ==4591== Address 0xa482958 is 24 bytes before a block of size 7 alloc'd
>>>> ==4591== at 0x4C2FF83: memalign (vg_replace_malloc.c:858)
>>>> ==4591== by 0x4FD121A: PetscMallocAlign (mal.c:28)
>>>> ==4591== by 0x4F31FB5: PetscStrallocpy (str.c:197)
>>>> ==4591== by 0x4F0D3F5: PetscClassRegLogRegister (classlog.c:253)
>>>> ==4591== by 0x4EF96E2: PetscClassIdRegister (plog.c:2053)
>>>> ==4591== by 0x51FA018: VecInitializePackage (dlregisvec.c:165)
>>>> ==4591== by 0x51F6DE9: VecCreate (veccreate.c:35)
>>>> ==4591== by 0x51C49F0: VecCreateSeq (vseqcr.c:37)
>>>> ==4591== by 0x5843191: MatSetUpMultiply_MPIAIJ (mmaij.c:104)
>>>> ==4591== by 0x5809943: MatAssemblyEnd_MPIAIJ (mpiaij.c:747)
>>>> ==4591== by 0x536B299: MatAssemblyEnd (matrix.c:5298)
>>>> ==4591== by 0x5829C05: MatLoad_MPIAIJ (mpiaij.c:3032)
>>>> ==4591== by 0x5337FEA: MatLoad (matrix.c:1101)
>>>> ==4591== by 0x400D9F: main (ex16.c:22)
>>>> ==4591==
>>>> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
>>>> [0]PETSC ERROR: Argument out of range
>>>> [0]PETSC ERROR: Column too large: col 96 max 35
>>>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
>>>> [0]PETSC ERROR: Petsc Development GIT revision: v3.7.4-1729-g4c4de23 GIT Date: 2016-10-20 22:22:58 +0000
>>>> [0]PETSC ERROR: ./ex16 on a arch-idx64-slu named asterix by balay Fri Oct 21 18:47:51 2016
>>>> [0]PETSC ERROR: Configure options --download-metis --download-parmetis --download-superlu_dist PETSC_ARCH=arch-idx64-slu
>>>> [0]PETSC ERROR: #1 MatSetValues_MPIAIJ() line 585 in /home/balay/petsc/src/mat/impls/aij/mpi/mpiaij.c
>>>> [0]PETSC ERROR: #2 MatAssemblyEnd_MPIAIJ() line 724 in /home/balay/petsc/src/mat/impls/aij/mpi/mpiaij.c
>>>> [0]PETSC ERROR: #3 MatAssemblyEnd() line 5298 in /home/balay/petsc/src/mat/interface/matrix.c
>>>> [0]PETSC ERROR: #4 MatView_MPIAIJ_ASCIIorDraworSocket() line 1410 in /home/balay/petsc/src/mat/impls/aij/mpi/mpiaij.c
>>>> [0]PETSC ERROR: #5 MatView_MPIAIJ() line 1440 in /home/balay/petsc/src/mat/impls/aij/mpi/mpiaij.c
>>>> [0]PETSC ERROR: #6 MatView() line 989 in /home/balay/petsc/src/mat/interface/matrix.c
>>>> [0]PETSC ERROR: #7 main() line 30 in /home/balay/download-pine/x/superlu_dist_test/ex16.c
>>>> [0]PETSC ERROR: PETSc Option Table entries:
>>>> [0]PETSC ERROR: -display :0.0
>>>> [0]PETSC ERROR: -f /home/balay/datafiles/matrices/small
>>>> [0]PETSC ERROR: -malloc_dump
>>>> [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov----------
>>>> application called MPI_Abort(MPI_COMM_WORLD, 63) - process 0
>>>> [cli_0]: aborting job:
>>>> application called MPI_Abort(MPI_COMM_WORLD, 63) - process 0
>>>> ==4591== 16,965 (2,744 direct, 14,221 indirect) bytes in 1 blocks are definitely lost in loss record 1,014 of 1,016
>>>> ==4591== at 0x4C2FF83: memalign (vg_replace_malloc.c:858)
>>>> ==4591== by 0x4FD121A: PetscMallocAlign (mal.c:28)
>>>> ==4591== by 0x52F3B14: MatCreate (gcreate.c:84)
>>>> ==4591== by 0x581390A: MatView_MPIAIJ_ASCIIorDraworSocket (mpiaij.c:1371)
>>>> ==4591== by 0x5814A75: MatView_MPIAIJ (mpiaij.c:1440)
>>>> ==4591== by 0x53373D7: MatView (matrix.c:989)
>>>> ==4591== by 0x40107E: main (ex16.c:30)
>>>> ==4591==
>>>>
>>>> ===================================================================================
>>>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>>> = PID 4591 RUNNING AT asterix
>>>> = EXIT CODE: 63
>>>> = CLEANING UP REMAINING PROCESSES
>>>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>> ===================================================================================
>>>> balay at asterix /home/balay/download-pine/x/superlu_dist_test
>>>> $
>>>
>
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